But remember, SkyWest's future is tied to a bankrupt "go with the lowest bidder" United (look what happened to Air Wisconsin!), and a possibly-bankrupt Delta. If Delta goes into bankrupcy, then SkyWest will be tied to two bankrupt carriers. They just recently lost the Continental codeshare in IAH.
As for them going at it alone, good luck. Look at Independence Air. But that pretty much goes for all regionals if they lose the codeshare, including Delta.
Yes, the Comair pay freeze sucks hard. But they still are coming out on top in pay and work rules. Also, they are union. I never liked unions, until now that I work under one. Also I think a positive is that they are wholly owned by Delta, as is ASA. In my opinion they could get sold off, but still continue to codeshare for Delta, just like happened here at XJT. But who knows what the future holds, anywhere.
SkyWest is a good company. I have friends there, and some great guys like Ophir and JDFlight have gotten hired there recently. There are a few things that I dislike about SkyWest though, like their 50/70 seat joint payscale, lack of a union, and no pay in training. I also really didn't take kindly to the comments made after they lost the CAL codeshare, how they'd "like to do business with CAL in 2007" which happens to be when our capacity purchase agreement is up at XJT with CAL. I KNOW Mesa, CHQ and SkyWest are armed and ready to try and swoop in and under-bid us.
Good luck to whatever you choose! I think your decision should be based on your personal desires and needs rather than politics or anyone else's opinion of a company. In 5 years everything could be drastically different, so you never know if a decision will be a good one. Go with what feels right.